The Scientist's Dilemma
by Skycloud26
Summary: Raphael saves a girl and can't get her out of his mind. He has a feeling that there's something special about her. When she is found hurt by his brothers, he takes her in and tries to better understand who she is, and why she's not afraid.
1. Chapter 1

Hey there! There are a few things that you should know about this story:

1. This is my first fan fic, so if you are going to criticize, do it constructively. Nobody looked this over, so there may be some errors.

2. Chapters may be long or short, depending on where I think a good stopping point might be.

3. It's rated M because there will be mature scenes in later chapters.

4. I don't TMNT. I own Hunter, so you can't use her.

5. Finally, I want you to enjoy!

Chapter 1

The scientist was working late with a container filled with a mysterious substance. It could mutate a living creature with a single touch. A small organism was crawling near her on the floor. She carried the open container to another counter. The little one bumped her leg, causing her to accidentally shake the container. A glob of the substance fell on the organism. It started to glow, then its body began to mutate. The scientist stepped back in horror as the creature cried in pain. Then it all stopped. The mutant looked up at the scientist with eyes filled with a mix of sadness and fear. She looked down at it and knew she had two choices. She could either take care of it or destroy it. She would never kill this creature or even think of hurting it. So she continued to raise the mutant and gave it lots of love. It had been a year and a half since the unfortunate accident when she found the cure. Well, not the permanent cure. According to the calculations, it would last 24 hours. She knew that she could make enough to last many years. She carefully filled a syringe with the dark purple liquid. She looked into the mutant's eyes and smiled. When it smiled back, she carefully injected the serum into its arm. The creature whined for a moment, then suddenly, it started to go back to normal. Its green skin turn back to a pale peach color. Its light purple eyes changed back to light brown. Soon it looked like it did before the mutating substance touched her. The scientist smiled at the little girl who looked at her with happiness. Every night at nine from then on, the scientist filled a test tube with the serum and let the girl drink it. When she was finally old enough, the scientist trusted the girl to take it by herself every night. Now the girl was 15. She was on a mission to locate the not-so mysterious substance mutagen. Containers were somehow scattered amongst the city. She had a high tech tracking device that was very accurate. She was lead down an alleyway until she reached the end, when she saw the container filled with the almost glowing blue-green liquid. She picked it up and scanned it so the tracker knew not to look for that one again. She happily put it in her purse. She was unaware of the pairs of eyes looking at her from the rooftop. She looked at her phone and saw that it was getting late. 8:45 to be exact. She search her purse for the serum. When she couldn't find it, she assumed that she left it at home. She wasn't planning to stay out that long, yet she was far away from her apartment. The subway might work, but she wouldn't risk changing in front of all the people. She had a skateboard, but even with it, it would take at least 25 minutes. She looked around, desperately trying to think of a way to return home in time. The eyes above her watched as she panicked. They didn't know why, so they kept watching her silently to hopefully find out. She looked down and saw a man hole cover. She sighed, and decided that if she did change, no one would see her. She carefully descended into the sewer and went in the direction of her home. The eyes on the rooftop were attached to four mutant creatures. They looked at each other in concern. Their home was down there. What if she found it. The tallest one spoke up. "Why did she have a container of mutagen?" he asked. "Why did she go in the sewer? I thought that humans thinks the sewer's gross," The shortest one asked. "I don't know," the first born said to both of them. "We should leave her alone. She could be dangerous to us. Let's just- where's Raphael?" The green eyed one had sneaked away to follow the girl. He was stealthily watched her as she tried to navigate through the maze of sewer tunnels. She did not know he was behind her, although she knew of the mutants. She spotted them months ago jumping across rooftops. After that she watched them from a distance, writing as much as she could about the four. She observed their behaviors, learning how they interact with each other. She noticed that the one in the blue seemed to be the leader and the one in red had to be second, because of the constant arguing. She also noticed red-masked one had some anger issues. She looked in her purse another time, then sighed in relief when she saw a test tube with a royal purple color liquid at the bottom. She quickly took it out and drank it. After putting the empty test tube back, she decided to keep going. The mutant creature wondered what was the substance she just drank. He continued to follow her in silence. She eventually found her self at what she thought was abandoned train tracks. She kept walking along the tracks when she heard a rumbling sound she stopped and listened to it. As it got louder, she turned around and saw a faint light. The tracks were not abandoned. She wanted to move but she was frozen in fear. The mutant looked at her wondering why she wasn't getting off the tracks. He saw that she still wasn't moving. The train was getting closer and closer. He figured that she wasn't moving because of fear, so right before the train could hit her, he ran up and pushed her off the tracks. She held still as the mutant pushed against her, trying to make sure she was safe. He was pressing her so much into the wall that she was having trouble breathing. The train was scraping his shell, so he tried to push against her more. When the train finally passed, he backed up. She took a deep breath, trying to take in more air. She looked at the mutant in front of her. It was one of the mutants that she had been watching. She was struggling for words since she was still trying to get over the initial shocks of almost being killed by a train and being this close to the creature. "Thank you... for saving me... from... the train," she said shakily. He gave her a half smile, not wanting to startle her more by talking. She started to walk away when he suddenly pinned her to the wall by holding her shoulders. "Uhh..." She didn't know why the mutant was keeping her there. He looked straight into her eyes, seeing a look of fear mixed with curiosity. He looked her over wanting to get a better look at her. She was wearing light colored skinny jeans, black sneakers, and a purple long sleeved shirt over a white cami. He carefully moved one of his hands to her collarbone so she wouldn't be able to get away. Then he took his other hand and ran it through her long, dirty blond hair. It was silky with no tangles. She felt him touching her hair, wondering what he wanted. She stayed perfectly still and silent, breathing slowly. She looked up at him and thought to herself, 'What is he doing? Why is he doing it?' He met her gaze with friendly eyes. Then he took his hands off her, backed up, and bolted. She watched his run off, not knowing if she would be this close to him again. She looked down and noticed that he dropped a weapon. Looking closer , she saw that it was a sai. She picked it up and then walked off in the other direction, climbed up to the surface, and walked through the night to go home


	2. Chapter 2

Chapter 2

She was putting on her running shoes when she noticed the sai on her nightstand. It had only been a month since the mutant turtle had saved her from the train. She rarely saw the creatures anymore. She kept looking for them, but they never showed up. Did they figure out that somebody was watching them? She wouldn't give up though. All she really wanted was to see the one who saved her. It was an amazing feeling being that close to him. Having him stroke her hair. She shook her head, trying to forget the thought for her current activity. She decided to go on a rooftop run. She was fast and agile from gymnastics, so jumping across buildings wasn't a challenge for her. She didn't do this every night, but often enough. She wanted to forget her problems. She wasn't popular. She was bullied for being a nerd. She was bullied so much that her mom took her out of school to be homeschooled. She took courses online during the day. It only took five hours each weekday, and with nobody to make fun of her, it was like paradise. She tied the laces in her her shoes, grabbed her maroon zip-up jacket and a water bottle, drank her medicine, and went up to the roof. She looked at the view of the city. There were lights everywhere and plenty of buildings. She backed up, then ran forward and jumped to the next building. She kept running and jumping, letting her problems slip away. After awhile she stopped on one roof and drank some water. There was a noise behind her so she quickly turned around. There was nothing there. She could've sworn that something made a noise. She turned back around and drank more of the water. The mutant swiftly hid on the fire escape. Hopefully she didn't see him. She may have not seen him in the past month, but he's seen her plenty. He looked back to see her throw the bottle into the trash can below, then jump to the next roof. He was going to keep following her when suddenly his phone started vibrating. "What is it Leo?" He asked with an annoyed tone. "Where are you Raph? We have scouting to do." "Relax, I'll be there in a minute. Nothing to worry about." He hung up and went in the direction of where his brothers were. She continued on her run across the city rooftops she felt a sharp pain in her upper arm. She noticed a throwing star near her feet. She looked at where the pain was coming from. Her eyes widen as she saw blood running down her arm. She took of her jacket and then put her hand over her wound. She looked up to see a figure at the other side of the building. As it got closer, she realized that it was a female ninja. A human one to be exact. She appeared to have short black hair, brown eyes, and she was outfitted in black with silver armor. "Hello there," she said, a hint a evil in voice. "I think you know about a certain group of mutant turtles." "Who are you?" She replied. " I don't know what you're talking about!" But she knew full well of what the ninja spoke of. "The name's Karai, and I know you're lying." She kept holding her arm tightly, trying to stop the blood. "I'm not lying," she said, desperately trying to get Karai to leave. "I've never seen or even heard of mutant turtles!" Karai glared at her, went behind her, then pulled out a small katana and put the blade up to the girl's neck, holding her uninjured arm to make sure she didn't try to run away. "I know you know about the turtles. I saw one following you the other day." The girl was surprised by the comment. One was following her? Was it the one that saved her from the train? Or maybe one of the others? "Tell me everything you know about the turtles, or else you'll die a painful death!" Karai demanded. Before the girl could say anything else, a throwing star landed at Karai's feet. That made her let go of the girl, who took a few steps back. "Leave her alone Karai!" The girl turned around to see one of the turtles. "Leonardo, so you do know this girl" Karai said. Leonardo looked over to girl, then back to Karai. " I have no idea who she is, and clearly, she doesn't know me either" he responded, pointing out how freaked out the girl looked. The wound seemed worse to her. She took her hand off the cut for a moment to see how bad it was. She quickly put it back with pressure, knowing that she shouldn't have taken it out in the first place. More and more blood continued to run down her left arm. She was hoping that it was a dream. Karai looked at the girl with a look that she read as " I'm not done with you", and then left in a puff of smoke.

Leo!" Another voice called, seeming to look for the blue-masked mutant. "Over here" Leo responded. Suddenly another mutant appeared. This one wearing a dark purple mask. "What happened," he asked Leo, apparently not noticing the girl standing about 10 feet away. Karai attacked this girl, thinking that we know her. The purple-masked turtle looked over and saw a girl shivering in fear, holding her arm. Then he saw blood covering the hand that was holding what must have been a wound from Karai. He went over to her. "Are you ok?" He asked, filled with concern for the girl. Rather than saying anything, she just shook her head no. "Leo, we have to help her. She's really hurt. If we can get her to the lair, I have supplies" he said to the other. "Shouldn't we just drop her off at a hospital? The people there would know how to take care if her, Donnie" Leo suggested. He was hesitant to bring her to the lair, since they didn't want humans to discover where they live. "We can't. The nearest hospital is miles away, and she needs attention right now" he responded. Almost as if she was trying to prove his point, the girl became lightheaded from the blood loss and fell to her knees. Donnie looked at Leo with worry in his eyes. "Alright, but I don't want Master Splinter to see her. I'll call the others to tell them to meet us there." Donnie picked up the jacket that she dropped. He started to wrap it around her arm. "The blood might stain the jacket" he said to the girl. "It's ok" she replied weakly. "I'll carry her back" Leo told Donnie, walking over to the faint girl. He picked her up and held her princess style.  
~ "Why do you think Leo called it off early tonight?" An orange-masked turtle asked. "I don't know and I don't care. All I know is that it's more time to not be around you" the green-eyed responded with a smirk. "Hurtful!" the other remarked. "Race you Raph!" he yelled as he bolted off. Raphael followed him, determined not to let his brother win.~

"Put her down here" said Donatello, pointing to the bean bag chair in his lab. Leo set her down carefully, making note that she less conscious then before. Donnie went to get supplies to help the gash in her arm. Splinter was meditating, so he did not hear his sons come in. Donnie came back and unwrapped the jacket so he could clean the injury. "Raph, Mikey, you're here" Leo said, seeing his brothers arrive home. "Why did... you call... us here?" Mikey said, out of breath from the race that he lost. "Follow me, I'll show you. But you have to be quiet" Leo instructed. The three went to the lab where they found their brother wrapping gauze around a human girl's arm. Raphael froze as he saw who the girl was. It was the girl he had saved. "Who is that?" Mikey whispered. "We don't know but-" "What happened to her" Raph interrupted, also trying to hid any sign of worry in his voice. Leo looked at him with an annoyed look, then said, "As I was saying, I caught Karai with her. She was going to kill her when I got there. She thought that we knew each other." Raph thought about why Karai thought this. Everything was fuzzy to her. She was contemplating if this was even real. The last thing she remembered before it all went black was the turtle with the red mask coming closer to her.


	3. Chapter 3

**I don't own TMNT. I just own Hunter.**

**Chapter 3**

She woke up in bed. She thought to herself that it all must have been a dream. Seeing the other mutants, hearing them talk, and getting her injury. But then her arm started to hurt. She saw it wrapped in layers of gauze with a small bloodstain in the middle. It wasn't a dream. At least not the injury. Then she looked around the room, noticing that it wasn't her own. It looked like it belonged to a teenage boy. It had posters of rock bands, a pizza box on the floor, and a drum set in the corner. She accepted reality. It wasn't a dream, everything had happened that night. Before she could make sense of anything else, the door started to open. She froze, staying still, not really knowing what would come in. It was the red-masked turtle. She relaxed a bit, but staying aware of the creature. "Mornin" he greeted her. "How you feelin?" She couldn't find any words. Then she finally just said quietly, "Fine." "Did you sleep ok?" "Yeah." "Good." He looked like he slept pretty bad. He was rubbing one of his shoulders, looking at one of his posters. "Is this your room?" she asked. "Yep" he replied, looking back at her. "Where'd you sleep then?" She was worried that maybe he was mad that she took his bed. He made a little grunt then answered. "In the main room. It wasn't comfy, but I managed." She felt much more comfortable around him for some reason. "Why am I in your room? Wouldn't you have rather slept in here instead?" She asked him. He looked like he didn't completely understand the question. He didn't know how to answer it. How was he supposed to tell her why without deteriorating his reputation? He thought about how to word it, then responded with, "I didn't think you wanted to wake up on a stone bench. But if you wanna go lie down there, I can give you a lift." He she smiled at the sarcastic comment. "I'm fine here, thanks" she said with a chuckle. He smiled back at her. "Oh, I never caught your name" she told him. "It's Raphael, but you can call me Raph." "That sounds like a tough guy name," she commented. "It's cool. I'm Hunter by the way." He remembered that Mikey was going to make breakfast. "Hey, so do want breakfast, cause Mikey's making it." "Sure, why not?" Raphael lead her out and to the kitchen. He saw that she had sort of a limp, so he let her lean on his arm. She could smell eggs and burnt toast. As she and Raphael waked in, she saw three others sitting at a table. "Guys, look! She's awake!" exclaimed the one with the light orange mask. The others turned towards her and smiled. "Hello" Hunter greeted. "Hi" they said in unison. The blue-masked one got up to greet her. "I should introduce myself," he started. "I'm Leonardo, that's Raphael," he pointed to Raph, who was still holding her up. "That's Donatello," he pointed to the one with the purple mask, " and that's Michelangelo" he pointed to the orange-masked one. "It's nice to meet you all" Hunter said. "I'm Hunter Aldaine." Raph lead her to the table and put her down on a stool. "Are you hungry?" Michelangelo asked Hunter. "Yeah, sure" she responded, remembering that all she had last night was a granola bar and that bottle of water. Mikey smiled and gave her a plate with the least burnt piece of toast and some eggs. "Thank you" she said. She saw that they were all just staring at her. She ate with her head down. It was probably the most awkward thing she had encountered in a long time. Finally, Raph broke the silence. "Stop staring at her guys! It's not like we haven't seen humans before." The others snapped out of their trance. "Who is this?" They all turned around to see Splinter standing behind Hunter. She looked at the tall mutant rat. She was having a hard time coping with the past 24 hours and now thought that another mutant was normal. Michelangelo stood up to introduce her. "That's Hunter ..." He had forgotten her last name. "Hunter Aldaine, Sir" Hunter told him. He looked at her closely, then right into her eyes. She stared back, trying to understand what he was doing. He stood back up and turned to Leonardo. "Why have you brought her here?" he asked, not liking the idea of strangers. "Karai attacked her last night. For some reason, she thought that we knew Hunter" Leo explained. Hunter knew why, but she wasn't just going to tell them that she had followed them. "Speaking of the attack," Donnie stated, " it looks like should change your bandages" he told her. She looked at the dried splotch of blood that had seeped through gauze. "Yeah, that would be good" she said quietly. "So can we keep her Sensei?" Mikey asked with excitement. They all turned to looked at the orange-masked turtle. Hunter gave him a strange look. 'Keep me? Like a pet?' she thought to herself. Almost as if he could read her thoughts, Mikey said "Not like a pet. I meant as a friend." He smiled at the last part. "Hmm.. I don't think she is threat to us. She seems very nice" Splinter decided. Hunter smiled. She had been accepted into the group. She decided to take this as an opportunity to observe the creatures. It would be great for her research.


	4. Chapter 4

Chapter 4

The whole day went by and nobody asked Hunter anything like 'where do you live?' or 'why were you on a roof?'. She could explain where she lived, but not so easily about the roof thing. She stayed down in the lair because Donnie had to check her arm every few hours. Now they had gone on their nightly patrol. But Raphael had stayed behind to keep her company. She was sitting with him on the bench. They were watching some episodes of Super Robo Mecha Force Five. Raph had been relatively quiet for a while. He noticed that Hunter was shivering. It _was_ pretty cold down there. "You cold?" he asked. She nodded. He promptly wrapped his arm around her and tucked his hand under the hurt arm, pulling her closer to him by her waist. It didn't help her a lot, but it was enough to stop shivering. When the episode ended, Hunter started to get up to put a new one in. Raph held her down and turned to look at her. "What's your deal?" he asked. "Excuse me?" Hunter wasn't sure how to answer. "Why are you acting so normal?" "Normal?" "Yeah. A regular person would be terrified of a giant mutant turtle. But you're acting like we're human!" Hunter couldn't tell him the real reason why mutants didn't scare her, so she came up with a believable statement. "You didn't give me a reason to be scared." Raph looked at her with confused eyes. "What do ya mean?" he wanted to know. "Well, you saved my life from the train," Hunter explained. "And without Leo and Donnie, Karai would've killed me." Raph gave her a smile. He was happy that a human wasn't scared of him. Especially that it was Hunter. She was nice and pretty and overall, fun to be around. Then the thought crossed his mind that he didn't want to share her. He saw her first. He _saved_ her first. He had the right not to share the girl, to keep her for himself. "Raphael," Hunter's voice interrupted his thoughts. "I think I should go home now. It's starting to get late, and I'm not sure how far it is from here." It was 8:00. Hunter had an hour left before the serum wore off. She wanted to get to it ASAP. "Ok, I'll go with you. It's dangerous at night" Raph said, letting her get out of his grasp. They went up to the streets and Hunter looked for a street sign. "583 Park Avenue" she said aloud. "Wow I'm really far away." "Where do ya live?" Raph asked. "In the Metropolitan Tower. On the upper east side." She told him. Raph thought about where this place was. Then he remembered April telling Donnie about it. "It's where the rich, snooty people live" she had said. "Yeah, that's pretty far off." He turned to look at Hunter, but she wasn't where she used to be. Now, she was halfway up a fire escape. "What are ya doing?" he asked her with a slight annoyed tone. "Going to the roof" she answered. "You can't just walk on the street or call a cab." "So you're just gonna jump building to building to get home?" "That's the plan!" she said, now standing on the roof, looking down at him. She was right. The guys took the Shell Raiser and he doubted that she could skateboard. "Wait up!" He called after her as she started her run. After a few miles of running across rooftops, Hunter slowed to a stop. "Why'd ya stop? We're not there yet" Raphael questioned. "I just want to rest for a bit" Hunter replied, breathing fast. "So," Raph started, "do your parents know where you've been?" "I actually just live with my mom, and no, she doesn't" Hunter told him, looking a bit guilty. "She should know. Well, at least make up an excuse." "I was going to tell her when she got back tomorrow night." "Tomorrow night?" Raph was confused. Where was her mother? "Yeah, she went to a convention in Virginia." Hunter didn't see the look if worry on his face. "So your mom left you all by yourself? How long has she been gone?" "About a week" she responded like it was normal. She saw the look on his face, and knew that what she just said sounded bad. "It's ok, I get money and there's always food in the fridge" she assured him. He still didn't look convinced. "What kinda convention is important enough to leave her daughter by herself? You could've been mugged and killed!" He was scared for her. She probably would have died if he and his brothers weren't there. "It's a mandatory thing" Hunter tried to explain. "She's a scientist. She needs to go to find out more about what she's researching." Raph started to relax a bit. "What's she researching?" he asked. Hunter was hesitant to tell him. She turned her head and looked at the ground. It was quiet for what seemed like hours. Finally, she told him. "She's working on a retro-mutagen serum to change all of the mutants back to normal." Raph looked at her in astonishment. 'Is that why she took that mutagen a while back? Her mom needed it?' he thought to him self. "Oh" was all he could manage to say. "So," Hunter started, trying to break the uncomfortable tension. "Do you happen to know what time it is?" He looked at her blankly for a few moments, still processing the new information he was given. Then he shook out of his trance and said, "Yeah, it's 8:25." Hunter had to hurry. She could almost feel the mutagen cells growing in her body. "Let's keep going, I think we're almost there" she said, trying to get him to go. They both went on, jumping across buildings until they finally got to hers. "Which floor is it?" asked Raphael. "This one" she said as she walked to the door from the large terrace. "The penthouse?" "Yeah, mom makes a lot of money from her research." Raph walked with her to the door when he decided to ask, " Do you .. like.. wanna meet up sometime?" Hunter smiled at him. "That would be great." She started to go in when she suddenly stopped. "Raph wait!" she exclaimed. "What's up?" he asked, turning back to face her. "Here's my number" she said, scribbling it down on a piece of scrap paper. "If you need anything, just give me a call." She handed it over to him with a suggestive smile. "Night Hunter" he said. "Night" she said back. With that, he jumped off the terrace to the next building and the next in order to get home. She went inside and got the medicine from her room. After she drank it, she realized that she was exhausted from the run, and decided to go to bed early. As she closed her eyes, she thought about the night when the red-masked mutant had saved her, and how his touch felt amazing. She finally fell asleep, wondering what his touch would be like when he knew what he was doing.


End file.
